How can I upload files to my multisite network sites I created with WP Empire Builder? The folder structure seems confusing
This is a well known WP multisite limitation (not caused by WP Empire Builder). It doesn't allow you uploading custom files to a root folder of a child site or to a custom folder other than "files".
The "files" folder of each site could be found at this path: wp-content/blogs.dir/{site_id}/files, where {site_id} is child site's ID number.